Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga13g01507.F4

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 3933
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34


Found at i:1113 original size:26 final size:26

Alignment explanation


    Indices: 1083--1166  Score: 73
    Period size: 26  Copynumber: 3.2  Consensus size: 26

       1073 TTGATGCAAG

                                      
       1083 TGTATAAAAAATAATTGATTTAAATA
          1 TGTATAAAAAATAATTGATTTAAATA

                     ***   *      **   *
       1109 TGTATATAATGTTAGTTTGA-TGCAA-G
          1 TGTATA-AAAAATA-ATTGATTTAAATA

                                      
       1135 TGTATAAAAAATAATTGATTTAAATA
          1 TGTATAAAAAATAATTGATTTAAATA

                  
       1161 TGTATA
          1 TGTATA

       1167 TAATGTTAAC


Statistics
Matches: 40,  Mismatches: 14, Indels: 8
        0.65            0.23        0.13

Matches are distributed among these distances:
  24    4  0.10
  25    7  0.17
  26   18  0.45
  27    7  0.17
  28    4  0.10

ACGTcount: A:0.45, C:0.01, G:0.13, T:0.40


Consensus pattern (26 bp):   
TGTATAAAAAATAATTGATTTAAATA

Found at i:1147 original size:52 final size:52

Alignment explanation


    Indices: 1069--1174  Score: 212
    Period size: 52  Copynumber: 2.0  Consensus size: 52

       1059 GACTCAGGTG

                                                                
       1069 TAGTTTGATGCAAGTGTATAAAAAATAATTGATTTAAATATGTATATAATGT
          1 TAGTTTGATGCAAGTGTATAAAAAATAATTGATTTAAATATGTATATAATGT

                                                                
       1121 TAGTTTGATGCAAGTGTATAAAAAATAATTGATTTAAATATGTATATAATGT
          1 TAGTTTGATGCAAGTGTATAAAAAATAATTGATTTAAATATGTATATAATGT

              
       1173 TA
          1 TA

       1175 ACTTCACTCT


Statistics
Matches: 54,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  52   54  1.00

ACGTcount: A:0.42, C:0.02, G:0.15, T:0.41


Consensus pattern (52 bp):   
TAGTTTGATGCAAGTGTATAAAAAATAATTGATTTAAATATGTATATAATGT

Found at i:1152 original size:24 final size:24

Alignment explanation


    Indices: 1073--1153  Score: 63
    Period size: 26  Copynumber: 3.2  Consensus size: 24

       1063 CAGGTGTAGT

                                    
       1073 TTGATGCAAGTGTATAAAAAATAA
          1 TTGATGCAAGTGTATAAAAAATAA

                  **   *         ***   *
       1097 TTGATTTAAATATGTATATAATGTTAGT
          1 TTGA-TGCAA-GTGTATA-AAAAATA-A

                                    
       1125 TTGATGCAAGTGTATAAAAAATAA
          1 TTGATGCAAGTGTATAAAAAATAA

                 
       1149 TTGAT
          1 TTGAT

       1154 TTAAATATGT


Statistics
Matches: 39,  Mismatches: 14, Indels: 8
        0.64            0.23        0.13

Matches are distributed among these distances:
  24    9  0.23
  25    7  0.18
  26   12  0.31
  27    7  0.18
  28    4  0.10

ACGTcount: A:0.43, C:0.02, G:0.16, T:0.38


Consensus pattern (24 bp):   
TTGATGCAAGTGTATAAAAAATAA
Done.